Abstract
The MicroArray Explorer (MAExplorer) is an open-source Java-based microarray data-mining tool that is available from the open source Web site as both a ready-to-run program and source code from http://maexplorer.sourceforge.net/. MAExplorer helps analyze expression patterns of individual genes, gene families, and clusters of genes. It is used as a stand-alone Java application and may be used for both ratio and intensity quantified array data (e.g., Cy3/Cy5, Affymetrix, and others). Data-mining sessions may be saved for continuation at later times or shared with collaborators; significant gene subsets, plots, and reports may be saved on the local disk. Extensions, called MAEPlugins, enable users to add new analysis methods and access to new genomic databases as they become available. MAExplorer was implemented in Java so that the same software could run on many platforms (e.g., Windows, MacOS 8/9 and X, Solaris, Linux, and Unix).
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References
Alizadeh A, Eisen MB, Davis RE, Ma C, Lossos IS, Rosenwald A, Boldrick JC, Sabet H, Tran T, Yu X, Powell JI, Yang L, Marti GE, Moore T, Hudson Jr J, Lu L, Lewis DB, Tibshirani R, Sherlock G, Chan WC, Greiner TC, Weissenburger DD, Armitage JO, Warnke R, Levy R, Wilson W, Grever MR, Byrd JHC, Botstein D, Brown PO, Staudt LM (2000). Distinct types of diffuse large B-cell lymphoma identified by gene expression profiling. Nature, 403:503–511.
Cleveland WS (1985). The Elements of Graphing Data. Wadsworth Press: Monterey, CA.
Cooper CS (2001). Applications of microarray technology in breast cancer research-Review. Breast Cancer Research, 3:158–175.
DeRisi J, Penland L, Brown PO, Bittner ML, Meltzer PS, Ray M, Chen Y, Su YA, Trent JM. (1996). Use of a cDNA microarray to analyze gene expression patterns in human cancer. Nature Genetics 14:457–460.
Dudoit S, Yang YH, Callow MJ, Speed TP (2000). Statistical methods for identifying differentially expressed genes in replicated microarray experiments. Technical Report No. TR-578 (August 2000). Department of Statistics, Stanford University: Stanford, CA.
Eisen MB, Spellman PT, Brown, PO, Botstein D (1998). Cluster analysis and display of genome-wide expression patterns. Proceedings of the National Academy of Science USA, 95:14863–14868.
Ermolaeva O, Rastogi M, Pruitt KD, Schuler GD, Bittner, Chen Y, Simon R, Meltzer P, Trent JM, Boguski MS (1998). Data management and analysis for gene expression arrays. Nature Genetics, 20:19–23.
Hughes TR, Marton MJ, Jones AR, Roberts CJ, Stoughton R, Armour CD, Bennett HA, Coffey E, Dai H, He YD, Kidd MJ, King AM, Meyer MR, Slade D, Lum PY (2000). Functional discovery via a compendium of expression profiles. Cell, 102:109–126.
Ideker T, Thorsson V, Ranish JA, Christmas R, Buhler J, Eng JK, Bumgarner R, Goodlet DR, Aebersold R, Hood L (2001). Integrated genomic and proteomic analyses of a systematically perturbed metabolic network. Science, 292:929–934.
Jagota A (2001). Microarray Data Analysis and Visualization. Bioinformatics By The Bay Press, Santa Cruz, CA.
Kerr MK, Churchill GA (2001). Statistical design and the analysis of gene expression microarray data. Genetical Research, 77:123–128.
Lemkin PF, Thornwall GC, Walton K, Hennighausen L (2000). The Microarray Explorer tool for data-mining of cDNA microarrays-application for the mammary gland. Nucleic Acids Research, 20:4452–4459.
Lemkin PF, Thornwall GC, Hennighausen L (2001). MicroArray Explorer-A Java-based tool for data-mining microarrays. AMS-IMSSIAM Summer Conference on Statistics in Functional Genomics, June 10–14, 2001. (http://www.lecb.ncifcrf.gov/MAExplorer/PDF/AMS-IMS-SIAM-Web-9-28-2001.pdf).
Schena M, Shalon D, Davis RW, Brown PO (1995). Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science, 270:467–470.
Schneiderman B (1997). Designing the Human Interface, 3rd ed. Addison-Wesley: New York.
Schulze A, Downward J (2001). Navigating gene expression using microarrays-A technology review. Nature Cell Biology, 3: E190–E195.
Simon R, Radmacher MD, Dobbin K (2001). Design of Studies Using DNA Microarrays. Technical Report #4.NCI, BRB: Rockville, MD.
Sneath PHA, Sokol RR (1973). Numerical Taxonomy. W.H. Freeman and Co: San Francisco.
Sorlie T, Perou CM, Tibshirani R, Aas T, Geisler S, Johnsen H, Hastie T, Eisen MB, van de Rijn M, Jeffrey SS, Thorsen T, Quist H, Matesse JC, Brown PO, Botstein D, Lonning PE, Borresen-Dale A-L (2001). Gene expression patterns of breast carcinomas distinguish tumor subclasses with clinical implications. Proceedings of the National Academy of Science USA, 98:10869–10874.
Strausberg RL, Austin MJF (1997). Functional genomics: Technological challenges and opportunities. Physiological Genomics, 1:25–32.
Tufte E (1997). Visual Explanations. Images and Quantities, Evidence and Narrative. Graphics Press: Cheshire, CT.
Tukey J (1977). Exploratory Data Analysis. Addison-Wesley: Reading, MA.
Weinstein JN, Myers TG, O’Conner PM, Friend SH, Fornace AJ, Kohn KW, Fojo T, Bates SE, Rubinstein LV, Anderson NL, Buolamwini JK, van Osdol WW, Monks AP, Scudiero DA, Sausville EA, Zaharevitz DW, Bunow B, Viswanadhan VN, Johynson GS, Wittes RE, Paull KD (1997). An information-intensive approach to the molecular pharmacology of cancer. Science, 275:343–349.
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Lemkin, P.F., Thornwall, G.C., Evans, J. (2003). Microarray Analysis Using the MicroArray Explorer. In: Parmigiani, G., Garrett, E.S., Irizarry, R.A., Zeger, S.L. (eds) The Analysis of Gene Expression Data. Statistics for Biology and Health. Springer, New York, NY. https://doi.org/10.1007/0-387-21679-0_10
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DOI: https://doi.org/10.1007/0-387-21679-0_10
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